Multiple sequence alignment - TraesCS3D01G378800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G378800 chr3D 100.000 3316 0 0 1 3316 495925388 495922073 0.000000e+00 6124.0
1 TraesCS3D01G378800 chr3D 86.364 110 10 4 2757 2861 495913978 495913869 7.520000e-22 115.0
2 TraesCS3D01G378800 chr3B 87.561 2854 144 76 3 2754 654658670 654655926 0.000000e+00 3109.0
3 TraesCS3D01G378800 chr3B 90.367 436 25 8 2889 3316 654655855 654655429 1.040000e-154 556.0
4 TraesCS3D01G378800 chr3A 85.624 2678 132 102 3 2564 635159093 635156553 0.000000e+00 2579.0
5 TraesCS3D01G378800 chr3A 85.012 427 22 19 2904 3316 635156478 635156080 2.400000e-106 396.0
6 TraesCS3D01G378800 chrUn 90.186 377 17 10 2889 3252 135235830 135235461 1.080000e-129 473.0
7 TraesCS3D01G378800 chrUn 92.466 146 10 1 2889 3034 158287229 158287085 1.210000e-49 207.0
8 TraesCS3D01G378800 chr7A 89.973 369 15 6 2077 2429 652985136 652985498 1.080000e-124 457.0
9 TraesCS3D01G378800 chr7A 87.736 106 8 3 2758 2858 710794346 710794451 5.810000e-23 119.0
10 TraesCS3D01G378800 chr7A 97.059 34 1 0 2384 2417 652985498 652985531 1.280000e-04 58.4
11 TraesCS3D01G378800 chr6D 95.062 81 4 0 2778 2858 132306954 132306874 9.660000e-26 128.0
12 TraesCS3D01G378800 chr6A 94.048 84 5 0 2778 2861 21747874 21747791 9.660000e-26 128.0
13 TraesCS3D01G378800 chr4D 94.048 84 5 0 2778 2861 17759662 17759579 9.660000e-26 128.0
14 TraesCS3D01G378800 chr4B 95.062 81 4 0 2778 2858 521730958 521731038 9.660000e-26 128.0
15 TraesCS3D01G378800 chr4A 95.062 81 4 0 2778 2858 649897961 649897881 9.660000e-26 128.0
16 TraesCS3D01G378800 chr2D 95.062 81 4 0 2778 2858 62385826 62385906 9.660000e-26 128.0
17 TraesCS3D01G378800 chr1D 95.062 81 4 0 2778 2858 476769088 476769008 9.660000e-26 128.0
18 TraesCS3D01G378800 chr5B 89.011 91 9 1 1162 1252 642840501 642840412 9.720000e-21 111.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G378800 chr3D 495922073 495925388 3315 True 6124.0 6124 100.000 1 3316 1 chr3D.!!$R2 3315
1 TraesCS3D01G378800 chr3B 654655429 654658670 3241 True 1832.5 3109 88.964 3 3316 2 chr3B.!!$R1 3313
2 TraesCS3D01G378800 chr3A 635156080 635159093 3013 True 1487.5 2579 85.318 3 3316 2 chr3A.!!$R1 3313

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
448 454 0.952010 TAAACCTCCCGAGCAAACGC 60.952 55.000 0.0 0.0 0.00 4.84 F
2207 2321 1.738099 CTGCAGCCACTGACCGTAC 60.738 63.158 0.0 0.0 32.44 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2235 2355 0.320421 CAGGAACCACCATCGTCGTT 60.320 55.0 0.00 0.00 42.04 3.85 R
3166 3328 0.467474 CATCATGAGGCCAGCCACAT 60.467 55.0 14.87 14.87 45.84 3.21 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.371126 GATGCTTTGAGTAATCTATAAGGGC 57.629 40.000 0.00 0.00 0.00 5.19
25 26 6.500589 TGCTTTGAGTAATCTATAAGGGCT 57.499 37.500 0.00 0.00 0.00 5.19
26 27 6.900194 TGCTTTGAGTAATCTATAAGGGCTT 58.100 36.000 0.00 0.00 0.00 4.35
27 28 6.992715 TGCTTTGAGTAATCTATAAGGGCTTC 59.007 38.462 0.00 0.00 0.00 3.86
40 41 1.976474 GGCTTCGAATGCCCAACCA 60.976 57.895 21.17 0.00 44.32 3.67
46 48 1.271934 TCGAATGCCCAACCATTTGTG 59.728 47.619 0.00 0.00 37.68 3.33
56 58 5.002516 CCCAACCATTTGTGTGCATATTTT 58.997 37.500 0.00 0.00 0.00 1.82
61 63 6.286758 ACCATTTGTGTGCATATTTTGTTCA 58.713 32.000 0.00 0.00 0.00 3.18
96 98 9.528018 AAATTTTGTGACTTCGATTACAAATGT 57.472 25.926 9.17 0.00 41.13 2.71
97 99 7.906611 TTTTGTGACTTCGATTACAAATGTG 57.093 32.000 9.17 0.00 41.13 3.21
99 101 6.466308 TGTGACTTCGATTACAAATGTGAG 57.534 37.500 0.00 0.00 0.00 3.51
100 102 6.220201 TGTGACTTCGATTACAAATGTGAGA 58.780 36.000 0.00 0.00 0.00 3.27
101 103 6.873605 TGTGACTTCGATTACAAATGTGAGAT 59.126 34.615 0.00 0.00 0.00 2.75
102 104 7.387673 TGTGACTTCGATTACAAATGTGAGATT 59.612 33.333 0.00 0.00 0.00 2.40
103 105 8.230486 GTGACTTCGATTACAAATGTGAGATTT 58.770 33.333 0.00 0.00 0.00 2.17
104 106 8.229811 TGACTTCGATTACAAATGTGAGATTTG 58.770 33.333 12.80 12.80 42.81 2.32
136 138 5.677091 GCATATTTTGAGCCAGAAATCACGT 60.677 40.000 0.00 0.00 0.00 4.49
176 178 6.916360 ATTTTGGTTCCTAGAAATGAAGCA 57.084 33.333 7.11 7.11 44.54 3.91
209 211 8.235905 TGCAAATAATTTTGAGCAATTTTAGGC 58.764 29.630 2.78 0.00 44.11 3.93
240 244 4.868171 TGTGTGATTTCTTAGCGGTACATC 59.132 41.667 0.00 0.00 0.00 3.06
254 258 3.443681 CGGTACATCTTGAAGCCCAAAAT 59.556 43.478 0.00 0.00 33.76 1.82
281 285 6.677920 GCACATAAAAAGGCACATCTTCGTAT 60.678 38.462 0.00 0.00 0.00 3.06
330 334 4.854399 TGCGAGTCAATTTACAAGTTTGG 58.146 39.130 0.00 0.00 0.00 3.28
356 360 3.964031 TGGCCTTTTACATTTGTCCAAGT 59.036 39.130 3.32 0.00 0.00 3.16
357 361 5.141182 TGGCCTTTTACATTTGTCCAAGTA 58.859 37.500 3.32 0.00 0.00 2.24
358 362 5.242838 TGGCCTTTTACATTTGTCCAAGTAG 59.757 40.000 3.32 0.00 0.00 2.57
359 363 5.243060 GGCCTTTTACATTTGTCCAAGTAGT 59.757 40.000 0.00 0.00 0.00 2.73
360 364 6.379386 GCCTTTTACATTTGTCCAAGTAGTC 58.621 40.000 0.00 0.00 0.00 2.59
361 365 6.569801 GCCTTTTACATTTGTCCAAGTAGTCC 60.570 42.308 0.00 0.00 0.00 3.85
362 366 6.715264 CCTTTTACATTTGTCCAAGTAGTCCT 59.285 38.462 0.00 0.00 0.00 3.85
363 367 7.881232 CCTTTTACATTTGTCCAAGTAGTCCTA 59.119 37.037 0.00 0.00 0.00 2.94
387 393 4.944962 TTAGATTTGTTCATGGAGCACG 57.055 40.909 0.00 0.00 0.00 5.34
394 400 1.461127 GTTCATGGAGCACGTCAAGAC 59.539 52.381 0.00 0.00 0.00 3.01
402 408 3.424962 GGAGCACGTCAAGACTTAATTGC 60.425 47.826 0.00 0.00 0.00 3.56
436 442 8.337741 GTAAATCGACTGATGTACTAAACCTC 57.662 38.462 0.00 0.00 40.68 3.85
437 443 4.978083 TCGACTGATGTACTAAACCTCC 57.022 45.455 0.00 0.00 0.00 4.30
438 444 3.698040 TCGACTGATGTACTAAACCTCCC 59.302 47.826 0.00 0.00 0.00 4.30
439 445 3.488721 CGACTGATGTACTAAACCTCCCG 60.489 52.174 0.00 0.00 0.00 5.14
440 446 3.698040 GACTGATGTACTAAACCTCCCGA 59.302 47.826 0.00 0.00 0.00 5.14
441 447 3.700038 ACTGATGTACTAAACCTCCCGAG 59.300 47.826 0.00 0.00 0.00 4.63
442 448 2.429610 TGATGTACTAAACCTCCCGAGC 59.570 50.000 0.00 0.00 0.00 5.03
443 449 1.927487 TGTACTAAACCTCCCGAGCA 58.073 50.000 0.00 0.00 0.00 4.26
444 450 2.250031 TGTACTAAACCTCCCGAGCAA 58.750 47.619 0.00 0.00 0.00 3.91
445 451 2.633967 TGTACTAAACCTCCCGAGCAAA 59.366 45.455 0.00 0.00 0.00 3.68
446 452 2.180432 ACTAAACCTCCCGAGCAAAC 57.820 50.000 0.00 0.00 0.00 2.93
447 453 1.076332 CTAAACCTCCCGAGCAAACG 58.924 55.000 0.00 0.00 0.00 3.60
448 454 0.952010 TAAACCTCCCGAGCAAACGC 60.952 55.000 0.00 0.00 0.00 4.84
479 485 2.490148 CCGCTGGCCACGATCTAGA 61.490 63.158 23.58 0.00 0.00 2.43
484 490 2.483714 GCTGGCCACGATCTAGAATTGA 60.484 50.000 0.00 0.00 0.00 2.57
485 491 3.388308 CTGGCCACGATCTAGAATTGAG 58.612 50.000 0.00 0.00 0.00 3.02
498 504 4.691860 AGAATTGAGGCGACATTTCTTG 57.308 40.909 14.21 0.00 37.26 3.02
505 512 4.338118 TGAGGCGACATTTCTTGAGTTTTT 59.662 37.500 0.00 0.00 0.00 1.94
509 516 4.219033 CGACATTTCTTGAGTTTTTCCCG 58.781 43.478 0.00 0.00 0.00 5.14
562 570 2.741878 GCTGCTTAATCTAGGCGGACAA 60.742 50.000 1.14 0.00 39.29 3.18
879 911 3.374402 CGTCGTGTCCCCAGCTCT 61.374 66.667 0.00 0.00 0.00 4.09
883 915 4.459089 GTGTCCCCAGCTCTCGCC 62.459 72.222 0.00 0.00 36.60 5.54
897 929 3.151022 CGCCCTCCTCTCCCACTC 61.151 72.222 0.00 0.00 0.00 3.51
978 1010 4.443457 CCAGCCCACGCTATATATATTGCT 60.443 45.833 21.53 10.04 46.25 3.91
1006 1038 4.116328 CGTCGGCTTCCAGCTCGA 62.116 66.667 5.55 5.55 41.99 4.04
1021 1053 3.900892 CGATCCCGACCTCACCGG 61.901 72.222 0.00 0.00 46.10 5.28
1052 1084 4.111016 CGCTGCGGACGGACTGTA 62.111 66.667 15.40 0.00 0.00 2.74
1053 1085 2.202623 GCTGCGGACGGACTGTAG 60.203 66.667 0.00 0.52 39.92 2.74
1054 1086 2.697761 GCTGCGGACGGACTGTAGA 61.698 63.158 8.38 0.00 39.43 2.59
1402 1434 3.636231 CTCGCCAGGTTGGTCCCA 61.636 66.667 0.00 0.00 40.46 4.37
1409 1441 4.660938 GGTTGGTCCCAGCCGCTT 62.661 66.667 3.27 0.00 37.56 4.68
1431 1484 2.192664 TCGCTTTATTCCAACAGGCA 57.807 45.000 0.00 0.00 0.00 4.75
1548 1641 7.735917 TCAGTCCTCTGTCTTCTTATTTTTGA 58.264 34.615 0.00 0.00 41.91 2.69
1863 1965 2.661537 CGGACGACAACAGCAGCA 60.662 61.111 0.00 0.00 0.00 4.41
2203 2317 2.046507 CCTCTGCAGCCACTGACC 60.047 66.667 9.47 0.00 32.44 4.02
2205 2319 3.231889 CTCTGCAGCCACTGACCGT 62.232 63.158 9.47 0.00 32.44 4.83
2206 2320 1.877576 CTCTGCAGCCACTGACCGTA 61.878 60.000 9.47 0.00 32.44 4.02
2207 2321 1.738099 CTGCAGCCACTGACCGTAC 60.738 63.158 0.00 0.00 32.44 3.67
2208 2322 2.434359 GCAGCCACTGACCGTACC 60.434 66.667 0.00 0.00 32.44 3.34
2210 2324 2.282674 AGCCACTGACCGTACCGA 60.283 61.111 0.00 0.00 0.00 4.69
2218 2338 2.436646 ACCGTACCGATCGACCGT 60.437 61.111 18.66 8.79 0.00 4.83
2221 2341 2.325857 GTACCGATCGACCGTCCG 59.674 66.667 18.66 0.00 0.00 4.79
2222 2342 2.173669 GTACCGATCGACCGTCCGA 61.174 63.158 18.66 0.00 43.16 4.55
2239 2359 3.635433 GACCCGATCGATGAAACGA 57.365 52.632 18.66 0.00 46.04 3.85
2240 2360 1.197910 GACCCGATCGATGAAACGAC 58.802 55.000 18.66 0.00 44.84 4.34
2362 2491 0.517316 GTAGGCGTCTTTTGCAGTGG 59.483 55.000 0.00 0.00 0.00 4.00
2399 2528 1.599606 CGGAGAGTGGAGTGGAGTGG 61.600 65.000 0.00 0.00 0.00 4.00
2400 2529 0.251832 GGAGAGTGGAGTGGAGTGGA 60.252 60.000 0.00 0.00 0.00 4.02
2401 2530 1.181786 GAGAGTGGAGTGGAGTGGAG 58.818 60.000 0.00 0.00 0.00 3.86
2402 2531 0.485099 AGAGTGGAGTGGAGTGGAGT 59.515 55.000 0.00 0.00 0.00 3.85
2403 2532 0.605589 GAGTGGAGTGGAGTGGAGTG 59.394 60.000 0.00 0.00 0.00 3.51
2463 2596 1.902938 ACTTCCTTTCTTGCTGGCTC 58.097 50.000 0.00 0.00 0.00 4.70
2464 2597 1.143684 ACTTCCTTTCTTGCTGGCTCA 59.856 47.619 0.00 0.00 0.00 4.26
2465 2598 1.538950 CTTCCTTTCTTGCTGGCTCAC 59.461 52.381 0.00 0.00 0.00 3.51
2466 2599 0.767375 TCCTTTCTTGCTGGCTCACT 59.233 50.000 0.00 0.00 0.00 3.41
2467 2600 1.163554 CCTTTCTTGCTGGCTCACTC 58.836 55.000 0.00 0.00 0.00 3.51
2468 2601 0.795085 CTTTCTTGCTGGCTCACTCG 59.205 55.000 0.00 0.00 0.00 4.18
2469 2602 1.230635 TTTCTTGCTGGCTCACTCGC 61.231 55.000 0.00 0.00 0.00 5.03
2470 2603 2.047465 CTTGCTGGCTCACTCGCT 60.047 61.111 0.00 0.00 0.00 4.93
2471 2604 2.357881 TTGCTGGCTCACTCGCTG 60.358 61.111 0.00 0.00 0.00 5.18
2473 2606 4.756458 GCTGGCTCACTCGCTGCT 62.756 66.667 0.00 0.00 0.00 4.24
2577 2716 1.673767 ACCAGAGACATGATGGGGTT 58.326 50.000 0.00 0.00 38.48 4.11
2583 2722 2.503356 GAGACATGATGGGGTTGAGACT 59.497 50.000 0.00 0.00 0.00 3.24
2584 2723 2.915604 AGACATGATGGGGTTGAGACTT 59.084 45.455 0.00 0.00 0.00 3.01
2590 2729 2.398754 TGGGGTTGAGACTTGAGAGA 57.601 50.000 0.00 0.00 0.00 3.10
2632 2785 3.857093 GGCTTGTTTGTACTGTTTGTGTG 59.143 43.478 0.00 0.00 0.00 3.82
2633 2786 4.481463 GCTTGTTTGTACTGTTTGTGTGT 58.519 39.130 0.00 0.00 0.00 3.72
2634 2787 4.323336 GCTTGTTTGTACTGTTTGTGTGTG 59.677 41.667 0.00 0.00 0.00 3.82
2635 2788 3.827625 TGTTTGTACTGTTTGTGTGTGC 58.172 40.909 0.00 0.00 0.00 4.57
2636 2789 3.253432 TGTTTGTACTGTTTGTGTGTGCA 59.747 39.130 0.00 0.00 0.00 4.57
2637 2790 3.755965 TTGTACTGTTTGTGTGTGCAG 57.244 42.857 0.00 0.00 35.31 4.41
2638 2791 2.013400 TGTACTGTTTGTGTGTGCAGG 58.987 47.619 0.00 0.00 33.62 4.85
2639 2792 1.333619 GTACTGTTTGTGTGTGCAGGG 59.666 52.381 0.00 0.00 33.62 4.45
2640 2793 1.037030 ACTGTTTGTGTGTGCAGGGG 61.037 55.000 0.00 0.00 33.62 4.79
2641 2794 0.751277 CTGTTTGTGTGTGCAGGGGA 60.751 55.000 0.00 0.00 0.00 4.81
2642 2795 0.751277 TGTTTGTGTGTGCAGGGGAG 60.751 55.000 0.00 0.00 0.00 4.30
2705 2858 2.840066 TTTCGTTGTTGCAGGGGCG 61.840 57.895 0.00 0.00 45.35 6.13
2754 2907 0.459489 TTTTTGTTTGCTCGCCTGCT 59.541 45.000 0.00 0.00 0.00 4.24
2755 2908 1.313772 TTTTGTTTGCTCGCCTGCTA 58.686 45.000 0.00 0.00 0.00 3.49
2756 2909 0.874390 TTTGTTTGCTCGCCTGCTAG 59.126 50.000 0.00 0.00 0.00 3.42
2757 2910 1.577328 TTGTTTGCTCGCCTGCTAGC 61.577 55.000 8.10 8.10 39.25 3.42
2758 2911 1.743252 GTTTGCTCGCCTGCTAGCT 60.743 57.895 17.23 0.00 39.53 3.32
2759 2912 0.460284 GTTTGCTCGCCTGCTAGCTA 60.460 55.000 17.23 6.47 39.53 3.32
2760 2913 0.460284 TTTGCTCGCCTGCTAGCTAC 60.460 55.000 17.23 4.21 39.53 3.58
2762 2915 1.007849 GCTCGCCTGCTAGCTACTC 60.008 63.158 17.23 1.71 35.80 2.59
2763 2916 1.657556 CTCGCCTGCTAGCTACTCC 59.342 63.158 17.23 0.00 0.00 3.85
2764 2917 1.801309 CTCGCCTGCTAGCTACTCCC 61.801 65.000 17.23 0.00 0.00 4.30
2765 2918 1.830408 CGCCTGCTAGCTACTCCCT 60.830 63.158 17.23 0.00 0.00 4.20
2766 2919 1.801309 CGCCTGCTAGCTACTCCCTC 61.801 65.000 17.23 0.00 0.00 4.30
2768 2921 1.175983 CCTGCTAGCTACTCCCTCCG 61.176 65.000 17.23 0.00 0.00 4.63
2769 2922 0.179015 CTGCTAGCTACTCCCTCCGA 60.179 60.000 17.23 0.00 0.00 4.55
2770 2923 0.257905 TGCTAGCTACTCCCTCCGAA 59.742 55.000 17.23 0.00 0.00 4.30
2771 2924 0.669619 GCTAGCTACTCCCTCCGAAC 59.330 60.000 7.70 0.00 0.00 3.95
2774 2927 0.611340 AGCTACTCCCTCCGAACGTT 60.611 55.000 0.00 0.00 0.00 3.99
2775 2928 0.179142 GCTACTCCCTCCGAACGTTC 60.179 60.000 18.47 18.47 0.00 3.95
2784 2937 2.427905 CGAACGTTCGGTCGCAGA 60.428 61.111 36.53 0.00 46.30 4.26
2785 2938 2.012414 CGAACGTTCGGTCGCAGAA 61.012 57.895 36.53 0.00 46.30 3.02
2787 2940 0.788391 GAACGTTCGGTCGCAGAAAT 59.212 50.000 13.36 0.00 39.69 2.17
2788 2941 0.511221 AACGTTCGGTCGCAGAAATG 59.489 50.000 0.00 0.00 39.69 2.32
2790 2943 1.011968 CGTTCGGTCGCAGAAATGGA 61.012 55.000 0.00 0.00 39.69 3.41
2791 2944 1.369625 GTTCGGTCGCAGAAATGGAT 58.630 50.000 0.00 0.00 39.69 3.41
2792 2945 2.546778 GTTCGGTCGCAGAAATGGATA 58.453 47.619 0.00 0.00 39.69 2.59
2794 2947 4.304110 GTTCGGTCGCAGAAATGGATATA 58.696 43.478 0.00 0.00 39.69 0.86
2795 2948 4.801330 TCGGTCGCAGAAATGGATATAT 57.199 40.909 0.00 0.00 39.69 0.86
2796 2949 4.744570 TCGGTCGCAGAAATGGATATATC 58.255 43.478 3.96 3.96 39.69 1.63
2797 2950 4.462834 TCGGTCGCAGAAATGGATATATCT 59.537 41.667 12.42 0.00 39.69 1.98
2798 2951 5.650703 TCGGTCGCAGAAATGGATATATCTA 59.349 40.000 12.42 6.97 39.69 1.98
2799 2952 5.974158 CGGTCGCAGAAATGGATATATCTAG 59.026 44.000 12.42 0.00 39.69 2.43
2800 2953 6.183360 CGGTCGCAGAAATGGATATATCTAGA 60.183 42.308 12.42 0.00 39.69 2.43
2801 2954 6.975772 GGTCGCAGAAATGGATATATCTAGAC 59.024 42.308 12.42 7.94 39.69 2.59
2803 2956 6.374613 TCGCAGAAATGGATATATCTAGACGT 59.625 38.462 12.42 0.00 0.00 4.34
2804 2957 7.551617 TCGCAGAAATGGATATATCTAGACGTA 59.448 37.037 12.42 0.00 0.00 3.57
2805 2958 8.346300 CGCAGAAATGGATATATCTAGACGTAT 58.654 37.037 12.42 0.00 0.00 3.06
2831 2984 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
2832 2985 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
2833 2986 7.361457 AGTTCTAGATACATCCATTTCCGAA 57.639 36.000 0.00 0.00 0.00 4.30
2834 2987 7.792032 AGTTCTAGATACATCCATTTCCGAAA 58.208 34.615 0.00 0.00 0.00 3.46
2835 2988 7.711339 AGTTCTAGATACATCCATTTCCGAAAC 59.289 37.037 0.00 0.00 0.00 2.78
2836 2989 7.119709 TCTAGATACATCCATTTCCGAAACA 57.880 36.000 0.00 0.00 0.00 2.83
2837 2990 7.561251 TCTAGATACATCCATTTCCGAAACAA 58.439 34.615 0.00 0.00 0.00 2.83
2838 2991 6.683974 AGATACATCCATTTCCGAAACAAG 57.316 37.500 0.00 0.00 0.00 3.16
2839 2992 6.180472 AGATACATCCATTTCCGAAACAAGT 58.820 36.000 0.00 0.00 0.00 3.16
2840 2993 7.335627 AGATACATCCATTTCCGAAACAAGTA 58.664 34.615 0.00 0.00 0.00 2.24
2841 2994 7.827236 AGATACATCCATTTCCGAAACAAGTAA 59.173 33.333 0.00 0.00 0.00 2.24
2842 2995 6.834168 ACATCCATTTCCGAAACAAGTAAT 57.166 33.333 0.00 0.00 0.00 1.89
2843 2996 7.227049 ACATCCATTTCCGAAACAAGTAATT 57.773 32.000 0.00 0.00 0.00 1.40
2844 2997 7.666623 ACATCCATTTCCGAAACAAGTAATTT 58.333 30.769 0.00 0.00 0.00 1.82
2845 2998 7.812669 ACATCCATTTCCGAAACAAGTAATTTC 59.187 33.333 0.00 0.00 33.52 2.17
2846 2999 7.278461 TCCATTTCCGAAACAAGTAATTTCA 57.722 32.000 0.00 0.00 36.09 2.69
2847 3000 7.717568 TCCATTTCCGAAACAAGTAATTTCAA 58.282 30.769 0.00 0.00 36.09 2.69
2848 3001 8.198109 TCCATTTCCGAAACAAGTAATTTCAAA 58.802 29.630 0.00 0.00 36.09 2.69
2849 3002 8.272866 CCATTTCCGAAACAAGTAATTTCAAAC 58.727 33.333 0.00 0.00 36.09 2.93
2850 3003 7.439204 TTTCCGAAACAAGTAATTTCAAACG 57.561 32.000 0.00 0.00 36.09 3.60
2851 3004 5.512473 TCCGAAACAAGTAATTTCAAACGG 58.488 37.500 0.00 0.00 36.09 4.44
2852 3005 5.296283 TCCGAAACAAGTAATTTCAAACGGA 59.704 36.000 0.00 0.00 41.49 4.69
2853 3006 5.623673 CCGAAACAAGTAATTTCAAACGGAG 59.376 40.000 0.00 0.00 36.09 4.63
2854 3007 6.423862 CGAAACAAGTAATTTCAAACGGAGA 58.576 36.000 0.00 0.00 36.09 3.71
2855 3008 6.573725 CGAAACAAGTAATTTCAAACGGAGAG 59.426 38.462 0.00 0.00 36.09 3.20
2856 3009 7.517734 CGAAACAAGTAATTTCAAACGGAGAGA 60.518 37.037 0.00 0.00 36.09 3.10
2857 3010 6.787085 ACAAGTAATTTCAAACGGAGAGAG 57.213 37.500 0.00 0.00 0.00 3.20
2858 3011 5.179555 ACAAGTAATTTCAAACGGAGAGAGC 59.820 40.000 0.00 0.00 0.00 4.09
2859 3012 4.894784 AGTAATTTCAAACGGAGAGAGCA 58.105 39.130 0.00 0.00 0.00 4.26
2860 3013 4.691216 AGTAATTTCAAACGGAGAGAGCAC 59.309 41.667 0.00 0.00 0.00 4.40
2861 3014 1.878953 TTTCAAACGGAGAGAGCACC 58.121 50.000 0.00 0.00 0.00 5.01
2865 3018 2.932234 AACGGAGAGAGCACCGGTG 61.932 63.158 30.66 30.66 46.59 4.94
2866 3019 4.135153 CGGAGAGAGCACCGGTGG 62.135 72.222 34.58 17.30 43.37 4.61
2867 3020 4.459089 GGAGAGAGCACCGGTGGC 62.459 72.222 34.58 25.54 0.00 5.01
2923 3076 7.415653 GGGCAAGAGAATATAGGTGAACTTTTG 60.416 40.741 0.00 0.00 0.00 2.44
2959 3112 4.620567 GCACTTTTGAACCCAACAACTTCT 60.621 41.667 0.00 0.00 30.88 2.85
2967 3120 0.035458 CCAACAACTTCTCCTCGCCT 59.965 55.000 0.00 0.00 0.00 5.52
3082 3236 2.505819 ACAAATGGAGACTAATCCGGCT 59.494 45.455 0.00 0.00 42.77 5.52
3083 3237 3.709653 ACAAATGGAGACTAATCCGGCTA 59.290 43.478 0.00 0.00 42.77 3.93
3163 3325 3.145228 GCTACTGCTGGTTGGAGAC 57.855 57.895 0.00 0.00 37.57 3.36
3164 3326 0.610687 GCTACTGCTGGTTGGAGACT 59.389 55.000 0.00 0.00 37.57 3.24
3166 3328 2.233922 GCTACTGCTGGTTGGAGACTAA 59.766 50.000 0.00 0.00 37.57 2.24
3167 3329 3.118592 GCTACTGCTGGTTGGAGACTAAT 60.119 47.826 0.00 0.00 37.57 1.73
3168 3330 3.340814 ACTGCTGGTTGGAGACTAATG 57.659 47.619 0.00 0.00 37.57 1.90
3170 3332 3.005554 CTGCTGGTTGGAGACTAATGTG 58.994 50.000 0.00 0.00 36.08 3.21
3171 3333 2.290260 TGCTGGTTGGAGACTAATGTGG 60.290 50.000 0.00 0.00 0.00 4.17
3172 3334 2.359900 CTGGTTGGAGACTAATGTGGC 58.640 52.381 0.00 0.00 0.00 5.01
3173 3335 1.985159 TGGTTGGAGACTAATGTGGCT 59.015 47.619 0.00 0.00 0.00 4.75
3258 3421 1.561643 TCAGTTCAGCCTAGTGAGGG 58.438 55.000 0.00 0.00 43.97 4.30
3272 3435 0.105194 TGAGGGCCCTAATCGATGGA 60.105 55.000 28.78 0.00 0.00 3.41
3276 3439 0.963962 GGCCCTAATCGATGGACGTA 59.036 55.000 0.00 0.00 43.13 3.57
3305 3468 2.226315 TGAGGTGATGGTGCTGCCT 61.226 57.895 0.00 0.00 38.35 4.75
3306 3469 1.001641 GAGGTGATGGTGCTGCCTT 60.002 57.895 0.00 0.00 38.35 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.164803 AGCCCTTATAGATTACTCAAAGCATC 58.835 38.462 0.00 0.00 0.00 3.91
1 2 7.084268 AGCCCTTATAGATTACTCAAAGCAT 57.916 36.000 0.00 0.00 0.00 3.79
9 10 6.166982 GCATTCGAAGCCCTTATAGATTACT 58.833 40.000 3.35 0.00 0.00 2.24
23 24 0.532115 AATGGTTGGGCATTCGAAGC 59.468 50.000 3.35 7.49 33.18 3.86
24 25 2.029110 ACAAATGGTTGGGCATTCGAAG 60.029 45.455 3.35 0.00 39.22 3.79
25 26 1.967066 ACAAATGGTTGGGCATTCGAA 59.033 42.857 0.00 0.00 39.22 3.71
26 27 1.271934 CACAAATGGTTGGGCATTCGA 59.728 47.619 0.00 0.00 39.22 3.71
27 28 1.000731 ACACAAATGGTTGGGCATTCG 59.999 47.619 0.00 0.00 42.36 3.34
70 72 9.528018 ACATTTGTAATCGAAGTCACAAAATTT 57.472 25.926 16.14 0.00 42.34 1.82
72 74 8.349245 TCACATTTGTAATCGAAGTCACAAAAT 58.651 29.630 16.14 8.77 42.34 1.82
79 81 8.443160 TCAAATCTCACATTTGTAATCGAAGTC 58.557 33.333 6.89 0.00 39.36 3.01
80 82 8.322906 TCAAATCTCACATTTGTAATCGAAGT 57.677 30.769 6.89 0.00 39.36 3.01
87 89 9.624697 GCAAACTATCAAATCTCACATTTGTAA 57.375 29.630 6.89 0.00 39.36 2.41
88 90 8.791675 TGCAAACTATCAAATCTCACATTTGTA 58.208 29.630 6.89 0.00 39.36 2.41
89 91 7.660112 TGCAAACTATCAAATCTCACATTTGT 58.340 30.769 6.89 0.00 39.36 2.83
90 92 8.697846 ATGCAAACTATCAAATCTCACATTTG 57.302 30.769 0.00 1.33 39.61 2.32
99 101 8.758715 GGCTCAAAATATGCAAACTATCAAATC 58.241 33.333 0.00 0.00 0.00 2.17
100 102 8.259411 TGGCTCAAAATATGCAAACTATCAAAT 58.741 29.630 0.00 0.00 0.00 2.32
101 103 7.609960 TGGCTCAAAATATGCAAACTATCAAA 58.390 30.769 0.00 0.00 0.00 2.69
102 104 7.122501 TCTGGCTCAAAATATGCAAACTATCAA 59.877 33.333 0.00 0.00 0.00 2.57
103 105 6.602803 TCTGGCTCAAAATATGCAAACTATCA 59.397 34.615 0.00 0.00 0.00 2.15
104 106 7.031226 TCTGGCTCAAAATATGCAAACTATC 57.969 36.000 0.00 0.00 0.00 2.08
108 110 6.591062 TGATTTCTGGCTCAAAATATGCAAAC 59.409 34.615 0.00 0.00 0.00 2.93
112 114 4.736793 CGTGATTTCTGGCTCAAAATATGC 59.263 41.667 0.00 0.00 0.00 3.14
152 154 7.301868 TGCTTCATTTCTAGGAACCAAAATT 57.698 32.000 0.00 0.00 0.00 1.82
162 164 8.706492 TTGCAATTTTATGCTTCATTTCTAGG 57.294 30.769 0.00 0.00 46.54 3.02
191 193 8.588472 AGTTCTAAGCCTAAAATTGCTCAAAAT 58.412 29.630 0.00 0.00 36.66 1.82
197 199 5.770162 ACACAGTTCTAAGCCTAAAATTGCT 59.230 36.000 0.00 0.00 40.17 3.91
209 211 6.183360 CCGCTAAGAAATCACACAGTTCTAAG 60.183 42.308 0.00 0.00 38.51 2.18
213 215 3.746492 ACCGCTAAGAAATCACACAGTTC 59.254 43.478 0.00 0.00 0.00 3.01
240 244 2.836262 TGTGCAATTTTGGGCTTCAAG 58.164 42.857 0.00 0.00 36.62 3.02
254 258 4.870123 AGATGTGCCTTTTTATGTGCAA 57.130 36.364 0.00 0.00 35.16 4.08
304 308 7.201478 CCAAACTTGTAAATTGACTCGCAAAAA 60.201 33.333 0.00 0.00 40.48 1.94
305 309 6.254589 CCAAACTTGTAAATTGACTCGCAAAA 59.745 34.615 0.00 0.00 40.48 2.44
306 310 5.746245 CCAAACTTGTAAATTGACTCGCAAA 59.254 36.000 0.00 0.00 40.48 3.68
307 311 5.066634 TCCAAACTTGTAAATTGACTCGCAA 59.933 36.000 0.00 0.00 41.53 4.85
308 312 4.576873 TCCAAACTTGTAAATTGACTCGCA 59.423 37.500 0.00 0.00 0.00 5.10
309 313 5.103290 TCCAAACTTGTAAATTGACTCGC 57.897 39.130 0.00 0.00 0.00 5.03
310 314 7.114811 CCAAATCCAAACTTGTAAATTGACTCG 59.885 37.037 0.00 0.00 0.00 4.18
311 315 7.095649 GCCAAATCCAAACTTGTAAATTGACTC 60.096 37.037 0.00 0.00 0.00 3.36
312 316 6.705825 GCCAAATCCAAACTTGTAAATTGACT 59.294 34.615 0.00 0.00 0.00 3.41
313 317 6.073276 GGCCAAATCCAAACTTGTAAATTGAC 60.073 38.462 0.00 0.00 0.00 3.18
330 334 5.546526 TGGACAAATGTAAAAGGCCAAATC 58.453 37.500 5.01 0.00 0.00 2.17
358 362 8.940952 GCTCCATGAACAAATCTAATATAGGAC 58.059 37.037 0.00 0.00 0.00 3.85
359 363 8.659527 TGCTCCATGAACAAATCTAATATAGGA 58.340 33.333 0.00 0.00 0.00 2.94
360 364 8.725148 GTGCTCCATGAACAAATCTAATATAGG 58.275 37.037 0.00 0.00 0.00 2.57
361 365 8.438513 CGTGCTCCATGAACAAATCTAATATAG 58.561 37.037 0.00 0.00 0.00 1.31
362 366 7.931407 ACGTGCTCCATGAACAAATCTAATATA 59.069 33.333 0.00 0.00 0.00 0.86
363 367 6.767902 ACGTGCTCCATGAACAAATCTAATAT 59.232 34.615 0.00 0.00 0.00 1.28
377 381 1.800805 AAGTCTTGACGTGCTCCATG 58.199 50.000 0.00 0.00 0.00 3.66
387 393 7.132863 ACTTTTTCTCGCAATTAAGTCTTGAC 58.867 34.615 0.00 0.00 0.00 3.18
394 400 8.776802 GTCGATTTACTTTTTCTCGCAATTAAG 58.223 33.333 0.00 0.00 0.00 1.85
402 408 7.050281 ACATCAGTCGATTTACTTTTTCTCG 57.950 36.000 0.00 0.00 0.00 4.04
430 436 2.258726 GCGTTTGCTCGGGAGGTTT 61.259 57.895 0.00 0.00 38.39 3.27
472 478 5.988561 AGAAATGTCGCCTCAATTCTAGATC 59.011 40.000 0.00 0.00 36.28 2.75
479 485 4.074970 ACTCAAGAAATGTCGCCTCAATT 58.925 39.130 0.00 0.00 0.00 2.32
484 490 4.261614 GGAAAAACTCAAGAAATGTCGCCT 60.262 41.667 0.00 0.00 0.00 5.52
485 491 3.981416 GGAAAAACTCAAGAAATGTCGCC 59.019 43.478 0.00 0.00 0.00 5.54
498 504 2.484651 GGCTTCTCTTCGGGAAAAACTC 59.515 50.000 0.00 0.00 0.00 3.01
505 512 1.131303 TTTGGGGCTTCTCTTCGGGA 61.131 55.000 0.00 0.00 0.00 5.14
531 538 2.101582 AGATTAAGCAGCGAGGGTACTG 59.898 50.000 0.00 0.00 36.96 2.74
562 570 3.383505 GGCTTTTTACACCACTGTTTCCT 59.616 43.478 0.00 0.00 0.00 3.36
879 911 3.663815 GAGTGGGAGAGGAGGGCGA 62.664 68.421 0.00 0.00 0.00 5.54
883 915 1.755008 GTCGGAGTGGGAGAGGAGG 60.755 68.421 0.00 0.00 0.00 4.30
884 916 1.755008 GGTCGGAGTGGGAGAGGAG 60.755 68.421 0.00 0.00 0.00 3.69
885 917 2.359404 GGTCGGAGTGGGAGAGGA 59.641 66.667 0.00 0.00 0.00 3.71
897 929 2.284699 ACAGGAGAAGGGGGTCGG 60.285 66.667 0.00 0.00 0.00 4.79
1039 1071 2.102553 GCTCTACAGTCCGTCCGC 59.897 66.667 0.00 0.00 0.00 5.54
1049 1081 0.538584 CACCATGGCTCTGCTCTACA 59.461 55.000 13.04 0.00 0.00 2.74
1050 1082 0.826715 TCACCATGGCTCTGCTCTAC 59.173 55.000 13.04 0.00 0.00 2.59
1051 1083 1.208052 GTTCACCATGGCTCTGCTCTA 59.792 52.381 13.04 0.00 0.00 2.43
1052 1084 0.035630 GTTCACCATGGCTCTGCTCT 60.036 55.000 13.04 0.00 0.00 4.09
1053 1085 1.364626 CGTTCACCATGGCTCTGCTC 61.365 60.000 13.04 0.00 0.00 4.26
1054 1086 1.376424 CGTTCACCATGGCTCTGCT 60.376 57.895 13.04 0.00 0.00 4.24
1402 1434 1.666189 GAATAAAGCGAAGAAGCGGCT 59.334 47.619 0.00 0.00 43.00 5.52
1409 1441 2.747446 GCCTGTTGGAATAAAGCGAAGA 59.253 45.455 0.00 0.00 34.57 2.87
1431 1484 5.273674 TCGAAAGAGAGATCATGATTGCT 57.726 39.130 10.14 10.10 34.84 3.91
1497 1563 1.069204 ACAGTGCAGAAAGAAGCTCGA 59.931 47.619 0.00 0.00 0.00 4.04
1499 1565 1.069364 GCACAGTGCAGAAAGAAGCTC 60.069 52.381 21.22 0.00 44.26 4.09
1501 1567 0.385223 CGCACAGTGCAGAAAGAAGC 60.385 55.000 25.19 0.00 45.36 3.86
1502 1568 1.220529 TCGCACAGTGCAGAAAGAAG 58.779 50.000 25.19 6.41 45.36 2.85
1548 1641 4.962155 ACGGAAGAGTTCAAGAAACAGAT 58.038 39.130 0.00 0.00 40.56 2.90
1855 1957 3.341043 CGTCGTTGCTGCTGCTGT 61.341 61.111 17.00 0.00 40.48 4.40
1856 1958 3.037833 TCGTCGTTGCTGCTGCTG 61.038 61.111 17.00 0.77 40.48 4.41
1863 1965 2.355481 GAACCCGTCGTCGTTGCT 60.355 61.111 0.71 0.00 35.01 3.91
2205 2319 2.173669 GTCGGACGGTCGATCGGTA 61.174 63.158 23.84 1.16 41.40 4.02
2206 2320 3.503363 GTCGGACGGTCGATCGGT 61.503 66.667 23.84 8.00 41.40 4.69
2207 2321 4.247612 GGTCGGACGGTCGATCGG 62.248 72.222 23.84 4.61 41.40 4.18
2208 2322 4.247612 GGGTCGGACGGTCGATCG 62.248 72.222 18.18 18.18 40.82 3.69
2210 2324 4.783621 TCGGGTCGGACGGTCGAT 62.784 66.667 13.12 0.00 41.40 3.59
2221 2341 1.197910 GTCGTTTCATCGATCGGGTC 58.802 55.000 16.41 0.00 41.78 4.46
2222 2342 0.524816 CGTCGTTTCATCGATCGGGT 60.525 55.000 16.41 1.25 41.78 5.28
2234 2354 0.395312 AGGAACCACCATCGTCGTTT 59.605 50.000 0.00 0.00 42.04 3.60
2235 2355 0.320421 CAGGAACCACCATCGTCGTT 60.320 55.000 0.00 0.00 42.04 3.85
2236 2356 1.292223 CAGGAACCACCATCGTCGT 59.708 57.895 0.00 0.00 42.04 4.34
2237 2357 0.736325 GACAGGAACCACCATCGTCG 60.736 60.000 0.00 0.00 42.04 5.12
2238 2358 0.736325 CGACAGGAACCACCATCGTC 60.736 60.000 0.00 0.00 41.48 4.20
2239 2359 1.292223 CGACAGGAACCACCATCGT 59.708 57.895 0.00 0.00 41.48 3.73
2240 2360 2.100631 GCGACAGGAACCACCATCG 61.101 63.158 0.00 0.00 45.82 3.84
2362 2491 4.101448 ATCCCAGACCGGCACTGC 62.101 66.667 19.67 0.00 34.47 4.40
2364 2493 3.461773 CGATCCCAGACCGGCACT 61.462 66.667 0.00 0.00 0.00 4.40
2399 2528 1.082756 CCAAAACGCTGCGACACTC 60.083 57.895 30.47 0.00 0.00 3.51
2400 2529 1.772063 GACCAAAACGCTGCGACACT 61.772 55.000 30.47 2.38 0.00 3.55
2401 2530 1.368850 GACCAAAACGCTGCGACAC 60.369 57.895 30.47 8.47 0.00 3.67
2402 2531 1.771073 CTGACCAAAACGCTGCGACA 61.771 55.000 30.47 14.01 0.00 4.35
2403 2532 1.082756 CTGACCAAAACGCTGCGAC 60.083 57.895 30.47 10.46 0.00 5.19
2468 2601 0.741221 GTACAGGGTACAGCAGCAGC 60.741 60.000 0.00 0.00 42.56 5.25
2469 2602 0.458543 CGTACAGGGTACAGCAGCAG 60.459 60.000 7.25 0.00 0.00 4.24
2470 2603 1.183030 ACGTACAGGGTACAGCAGCA 61.183 55.000 7.25 0.00 0.00 4.41
2471 2604 0.813184 TACGTACAGGGTACAGCAGC 59.187 55.000 7.25 0.00 0.00 5.25
2472 2605 1.202110 CGTACGTACAGGGTACAGCAG 60.202 57.143 24.50 0.81 40.13 4.24
2473 2606 0.804364 CGTACGTACAGGGTACAGCA 59.196 55.000 24.50 0.00 40.13 4.41
2577 2716 4.671831 ACCATCTCTTCTCTCAAGTCTCA 58.328 43.478 0.00 0.00 0.00 3.27
2583 2722 2.171003 TGCGACCATCTCTTCTCTCAA 58.829 47.619 0.00 0.00 0.00 3.02
2584 2723 1.839424 TGCGACCATCTCTTCTCTCA 58.161 50.000 0.00 0.00 0.00 3.27
2590 2729 3.077359 CCTTTTCTTGCGACCATCTCTT 58.923 45.455 0.00 0.00 0.00 2.85
2614 2753 3.253432 TGCACACACAAACAGTACAAACA 59.747 39.130 0.00 0.00 0.00 2.83
2636 2789 4.814041 GAGCTGCCTCCCTCCCCT 62.814 72.222 0.00 0.00 31.68 4.79
2642 2795 4.785453 CAACCCGAGCTGCCTCCC 62.785 72.222 0.00 0.00 34.49 4.30
2652 2805 3.068691 CCCTCTCGCTCAACCCGA 61.069 66.667 0.00 0.00 0.00 5.14
2656 2809 1.546476 TCTCTTTCCCTCTCGCTCAAC 59.454 52.381 0.00 0.00 0.00 3.18
2721 2874 1.202405 ACAAAAAGCAGCCTTTCGTGG 60.202 47.619 0.00 0.00 40.30 4.94
2754 2907 0.254178 ACGTTCGGAGGGAGTAGCTA 59.746 55.000 0.00 0.00 0.00 3.32
2755 2908 0.611340 AACGTTCGGAGGGAGTAGCT 60.611 55.000 0.00 0.00 0.00 3.32
2756 2909 0.179142 GAACGTTCGGAGGGAGTAGC 60.179 60.000 13.36 0.00 0.00 3.58
2757 2910 0.098376 CGAACGTTCGGAGGGAGTAG 59.902 60.000 36.53 10.09 46.30 2.57
2758 2911 2.174334 CGAACGTTCGGAGGGAGTA 58.826 57.895 36.53 0.00 46.30 2.59
2759 2912 2.960170 CGAACGTTCGGAGGGAGT 59.040 61.111 36.53 0.00 46.30 3.85
2768 2921 0.788391 ATTTCTGCGACCGAACGTTC 59.212 50.000 18.47 18.47 35.59 3.95
2769 2922 0.511221 CATTTCTGCGACCGAACGTT 59.489 50.000 0.00 0.00 35.59 3.99
2770 2923 1.289109 CCATTTCTGCGACCGAACGT 61.289 55.000 0.00 0.00 35.59 3.99
2771 2924 1.011968 TCCATTTCTGCGACCGAACG 61.012 55.000 0.00 0.00 0.00 3.95
2774 2927 4.462834 AGATATATCCATTTCTGCGACCGA 59.537 41.667 9.18 0.00 0.00 4.69
2775 2928 4.748892 AGATATATCCATTTCTGCGACCG 58.251 43.478 9.18 0.00 0.00 4.79
2777 2930 6.689241 CGTCTAGATATATCCATTTCTGCGAC 59.311 42.308 9.18 2.25 0.00 5.19
2778 2931 6.374613 ACGTCTAGATATATCCATTTCTGCGA 59.625 38.462 9.18 0.00 0.00 5.10
2779 2932 6.556212 ACGTCTAGATATATCCATTTCTGCG 58.444 40.000 9.18 6.40 0.00 5.18
2805 2958 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
2806 2959 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
2807 2960 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
2809 2962 6.978674 TCGGAAATGGATGTATCTAGAACT 57.021 37.500 0.00 0.00 0.00 3.01
2810 2963 7.494625 TGTTTCGGAAATGGATGTATCTAGAAC 59.505 37.037 6.43 0.00 0.00 3.01
2811 2964 7.561251 TGTTTCGGAAATGGATGTATCTAGAA 58.439 34.615 6.43 0.00 0.00 2.10
2812 2965 7.119709 TGTTTCGGAAATGGATGTATCTAGA 57.880 36.000 6.43 0.00 0.00 2.43
2813 2966 7.495934 ACTTGTTTCGGAAATGGATGTATCTAG 59.504 37.037 6.43 0.24 0.00 2.43
2814 2967 7.335627 ACTTGTTTCGGAAATGGATGTATCTA 58.664 34.615 6.43 0.00 0.00 1.98
2815 2968 6.180472 ACTTGTTTCGGAAATGGATGTATCT 58.820 36.000 6.43 0.00 0.00 1.98
2816 2969 6.436843 ACTTGTTTCGGAAATGGATGTATC 57.563 37.500 6.43 0.00 0.00 2.24
2817 2970 7.931578 TTACTTGTTTCGGAAATGGATGTAT 57.068 32.000 6.43 0.00 0.00 2.29
2818 2971 7.931578 ATTACTTGTTTCGGAAATGGATGTA 57.068 32.000 6.43 4.67 0.00 2.29
2819 2972 6.834168 ATTACTTGTTTCGGAAATGGATGT 57.166 33.333 6.43 5.48 0.00 3.06
2820 2973 7.812191 TGAAATTACTTGTTTCGGAAATGGATG 59.188 33.333 6.43 0.23 38.18 3.51
2821 2974 7.891561 TGAAATTACTTGTTTCGGAAATGGAT 58.108 30.769 6.43 0.00 38.18 3.41
2822 2975 7.278461 TGAAATTACTTGTTTCGGAAATGGA 57.722 32.000 6.43 0.00 38.18 3.41
2823 2976 7.938563 TTGAAATTACTTGTTTCGGAAATGG 57.061 32.000 6.43 3.13 38.18 3.16
2824 2977 7.995998 CGTTTGAAATTACTTGTTTCGGAAATG 59.004 33.333 6.43 3.45 38.18 2.32
2825 2978 7.168469 CCGTTTGAAATTACTTGTTTCGGAAAT 59.832 33.333 6.43 0.00 38.18 2.17
2826 2979 6.472808 CCGTTTGAAATTACTTGTTTCGGAAA 59.527 34.615 0.00 0.00 38.18 3.13
2827 2980 5.972382 CCGTTTGAAATTACTTGTTTCGGAA 59.028 36.000 0.00 0.00 38.18 4.30
2828 2981 5.296283 TCCGTTTGAAATTACTTGTTTCGGA 59.704 36.000 0.00 0.00 38.18 4.55
2829 2982 5.512473 TCCGTTTGAAATTACTTGTTTCGG 58.488 37.500 0.00 0.00 38.18 4.30
2830 2983 6.423862 TCTCCGTTTGAAATTACTTGTTTCG 58.576 36.000 0.00 0.00 38.18 3.46
2831 2984 7.636326 TCTCTCCGTTTGAAATTACTTGTTTC 58.364 34.615 0.00 0.00 36.39 2.78
2832 2985 7.562454 TCTCTCCGTTTGAAATTACTTGTTT 57.438 32.000 0.00 0.00 0.00 2.83
2833 2986 6.293462 GCTCTCTCCGTTTGAAATTACTTGTT 60.293 38.462 0.00 0.00 0.00 2.83
2834 2987 5.179555 GCTCTCTCCGTTTGAAATTACTTGT 59.820 40.000 0.00 0.00 0.00 3.16
2835 2988 5.179368 TGCTCTCTCCGTTTGAAATTACTTG 59.821 40.000 0.00 0.00 0.00 3.16
2836 2989 5.179555 GTGCTCTCTCCGTTTGAAATTACTT 59.820 40.000 0.00 0.00 0.00 2.24
2837 2990 4.691216 GTGCTCTCTCCGTTTGAAATTACT 59.309 41.667 0.00 0.00 0.00 2.24
2838 2991 4.142881 GGTGCTCTCTCCGTTTGAAATTAC 60.143 45.833 0.00 0.00 0.00 1.89
2839 2992 4.000988 GGTGCTCTCTCCGTTTGAAATTA 58.999 43.478 0.00 0.00 0.00 1.40
2840 2993 2.814336 GGTGCTCTCTCCGTTTGAAATT 59.186 45.455 0.00 0.00 0.00 1.82
2841 2994 2.427506 GGTGCTCTCTCCGTTTGAAAT 58.572 47.619 0.00 0.00 0.00 2.17
2842 2995 1.872237 CGGTGCTCTCTCCGTTTGAAA 60.872 52.381 0.00 0.00 42.56 2.69
2843 2996 0.319555 CGGTGCTCTCTCCGTTTGAA 60.320 55.000 0.00 0.00 42.56 2.69
2844 2997 1.289066 CGGTGCTCTCTCCGTTTGA 59.711 57.895 0.00 0.00 42.56 2.69
2845 2998 1.738099 CCGGTGCTCTCTCCGTTTG 60.738 63.158 0.00 0.00 45.14 2.93
2846 2999 2.207924 ACCGGTGCTCTCTCCGTTT 61.208 57.895 6.12 0.00 45.14 3.60
2847 3000 2.600769 ACCGGTGCTCTCTCCGTT 60.601 61.111 6.12 0.00 45.14 4.44
2848 3001 3.374402 CACCGGTGCTCTCTCCGT 61.374 66.667 24.02 0.00 45.14 4.69
2849 3002 4.135153 CCACCGGTGCTCTCTCCG 62.135 72.222 29.75 9.01 45.91 4.63
2850 3003 4.459089 GCCACCGGTGCTCTCTCC 62.459 72.222 29.75 6.55 0.00 3.71
2851 3004 4.803426 CGCCACCGGTGCTCTCTC 62.803 72.222 29.75 11.36 0.00 3.20
2858 3011 4.602259 ACACAGACGCCACCGGTG 62.602 66.667 28.26 28.26 39.22 4.94
2859 3012 4.295119 GACACAGACGCCACCGGT 62.295 66.667 0.00 0.00 39.22 5.28
2860 3013 3.991051 AGACACAGACGCCACCGG 61.991 66.667 0.00 0.00 39.22 5.28
2861 3014 2.734723 CAGACACAGACGCCACCG 60.735 66.667 0.00 0.00 41.14 4.94
2862 3015 1.664965 GACAGACACAGACGCCACC 60.665 63.158 0.00 0.00 0.00 4.61
2863 3016 1.067416 TGACAGACACAGACGCCAC 59.933 57.895 0.00 0.00 0.00 5.01
2864 3017 3.532501 TGACAGACACAGACGCCA 58.467 55.556 0.00 0.00 0.00 5.69
2886 3039 3.698820 CTTGCCCTTGCCCTTGCC 61.699 66.667 0.00 0.00 36.33 4.52
2887 3040 2.601367 TCTTGCCCTTGCCCTTGC 60.601 61.111 0.00 0.00 36.33 4.01
2888 3041 0.540365 TTCTCTTGCCCTTGCCCTTG 60.540 55.000 0.00 0.00 36.33 3.61
2923 3076 5.235305 TCAAAAGTGCAAAGAGTGAGAAC 57.765 39.130 0.00 0.00 0.00 3.01
2929 3082 3.096092 TGGGTTCAAAAGTGCAAAGAGT 58.904 40.909 0.00 0.00 0.00 3.24
2967 3120 3.049674 CTTGAAGCCGAAGCCGCA 61.050 61.111 0.00 0.00 41.25 5.69
3024 3177 2.056223 GTGCAGATGCCCCATGCTT 61.056 57.895 1.72 0.00 40.62 3.91
3162 3324 0.921896 ATGAGGCCAGCCACATTAGT 59.078 50.000 14.87 0.00 43.17 2.24
3163 3325 1.134007 TCATGAGGCCAGCCACATTAG 60.134 52.381 17.56 8.99 43.17 1.73
3164 3326 0.918258 TCATGAGGCCAGCCACATTA 59.082 50.000 17.56 8.64 43.17 1.90
3166 3328 0.467474 CATCATGAGGCCAGCCACAT 60.467 55.000 14.87 14.87 45.84 3.21
3167 3329 1.077285 CATCATGAGGCCAGCCACA 60.077 57.895 11.28 11.28 40.71 4.17
3168 3330 0.682209 AACATCATGAGGCCAGCCAC 60.682 55.000 12.03 5.16 38.92 5.01
3170 3332 2.057137 TTAACATCATGAGGCCAGCC 57.943 50.000 7.40 0.00 0.00 4.85
3171 3333 2.954318 ACATTAACATCATGAGGCCAGC 59.046 45.455 7.40 0.00 0.00 4.85
3172 3334 4.458397 AGACATTAACATCATGAGGCCAG 58.542 43.478 7.40 0.00 0.00 4.85
3173 3335 4.080413 TGAGACATTAACATCATGAGGCCA 60.080 41.667 7.40 0.00 0.00 5.36
3251 3414 1.051812 CATCGATTAGGGCCCTCACT 58.948 55.000 32.80 14.79 0.00 3.41
3258 3421 2.607187 CATACGTCCATCGATTAGGGC 58.393 52.381 0.00 0.00 42.86 5.19
3272 3435 2.103373 ACCTCACTGATCAGCATACGT 58.897 47.619 22.83 9.61 0.00 3.57
3276 3439 2.158798 CCATCACCTCACTGATCAGCAT 60.159 50.000 22.83 0.73 0.00 3.79


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.